Bacterial and archaeal communities were characterized from groundwater, seawater and sediment samples related to submarine groundwater discharge site on the south coast of Finland. Illumina MiSeq platform with paired-end read protocol was used to obtain the sequences. Samples were retrieved from two groundwater wells near-shore, seawater 1 m above seafloor of three previously detected pockmarks (B,D,E) and control site further from the shore. Sediment samples were retrieved from two depths of each pockmark, 1.5-2.5 cm and 3.5 to 4.5 cm. Duplicate samples (a,b) were taken from each sampling point, and seawater samples were filtered first through 0.2 um filters, flowthrough was combined from a and b and filtered again through 0.1 um filter.